data_3TQ3
#
_model_server_result.job_id            DahRXc9oPVH9hoqOOCZOJw 
_model_server_result.datetime_utc      '2025-03-03 00:26:02' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          3tq3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":777}' 
#
_entry.id    3TQ3 
#
_exptl.entry_id    3TQ3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            3TQ3 
_cell.length_a            60.594 
_cell.length_b            60.594 
_cell.length_c            64.146 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TQ3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.594 104.951887 0 
3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.594 104.951887 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 C O1A DUP . A DUP 153 1_555 D MG MG . A MG 154 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.931 ? 
metalc ? metalc2 C O2G DUP . A DUP 153 1_555 D MG MG . A MG 154 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc3 C O1B DUP . A DUP 153 1_555 D MG MG . A MG 154 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc4 D MG MG . A MG 154 1_555 E O HOH . A HOH 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc5 D MG MG . A MG 154 1_555 E O HOH . A HOH 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc6 D MG MG . A MG 154 1_555 B OP1 UMP . A UMP 777 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.524 ? 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N1 C2 UMP sing 403 n n 
N1 C6 UMP sing 404 n n 
N1 C1' UMP sing 405 n n 
C2 N3 UMP sing 406 n n 
C2 O2 UMP doub 407 n n 
N3 C4 UMP sing 408 n n 
N3 HN3 UMP sing 409 n n 
C4 C5 UMP sing 410 n n 
C4 O4 UMP doub 411 n n 
C5 C6 UMP doub 412 n n 
C5 H5 UMP sing 413 n n 
C6 H6 UMP sing 414 n n 
C1' C2' UMP sing 415 n n 
C1' O4' UMP sing 416 n n 
C1' H1' UMP sing 417 n n 
C2' C3' UMP sing 418 n n 
C2' H2' UMP sing 419 n n 
C2' "H2''" UMP sing 420 n n 
C3' C4' UMP sing 421 n n 
C3' O3' UMP sing 422 n n 
C3' H3' UMP sing 423 n n 
C4' O4' UMP sing 424 n n 
C4' C5' UMP sing 425 n n 
C4' H4' UMP sing 426 n n 
O3' HO3' UMP sing 427 n n 
C5' O5' UMP sing 428 n n 
C5' H5' UMP sing 429 n n 
C5' "H5''" UMP sing 430 n n 
O5' P UMP sing 431 n n 
P OP1 UMP doub 432 n n 
P OP2 UMP sing 433 n n 
P OP3 UMP sing 434 n n 
OP2 HOP2 UMP sing 435 n n 
OP3 HOP3 UMP sing 436 n n 
#
_atom_sites.entry_id                     3TQ3 
_atom_sites.fract_transf_matrix[1][1]    0.016503 
_atom_sites.fract_transf_matrix[1][2]    0.009528 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019056 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.015589 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 UMP A 1 777 777 UMP UMP . 
C 3 DUP A 1 153 777 DUP DUP . 
D 4 MG A 1 154 1 MG MG . 
E 5 HOH A 1 155 1 HOH HOH . 
E 5 HOH A 2 156 2 HOH HOH . 
E 5 HOH A 3 157 3 HOH HOH . 
E 5 HOH A 4 158 4 HOH HOH . 
E 5 HOH A 5 159 5 HOH HOH . 
E 5 HOH A 6 160 6 HOH HOH . 
E 5 HOH A 7 161 7 HOH HOH . 
E 5 HOH A 8 162 8 HOH HOH . 
E 5 HOH A 9 163 9 HOH HOH . 
E 5 HOH A 10 164 10 HOH HOH . 
E 5 HOH A 11 165 11 HOH HOH . 
E 5 HOH A 12 166 12 HOH HOH . 
E 5 HOH A 13 167 13 HOH HOH . 
E 5 HOH A 14 168 14 HOH HOH . 
E 5 HOH A 15 169 15 HOH HOH . 
E 5 HOH A 16 170 16 HOH HOH . 
E 5 HOH A 17 171 17 HOH HOH . 
E 5 HOH A 18 172 18 HOH HOH . 
E 5 HOH A 19 173 19 HOH HOH . 
E 5 HOH A 20 174 20 HOH HOH . 
E 5 HOH A 21 175 21 HOH HOH . 
E 5 HOH A 22 176 22 HOH HOH . 
E 5 HOH A 23 177 23 HOH HOH . 
E 5 HOH A 24 178 24 HOH HOH . 
E 5 HOH A 25 179 25 HOH HOH . 
E 5 HOH A 26 180 26 HOH HOH . 
E 5 HOH A 27 181 27 HOH HOH . 
E 5 HOH A 28 182 28 HOH HOH . 
E 5 HOH A 29 183 29 HOH HOH . 
E 5 HOH A 30 184 30 HOH HOH . 
E 5 HOH A 31 185 31 HOH HOH . 
E 5 HOH A 32 186 32 HOH HOH . 
E 5 HOH A 33 187 33 HOH HOH . 
E 5 HOH A 34 188 34 HOH HOH . 
E 5 HOH A 35 189 35 HOH HOH . 
E 5 HOH A 36 190 36 HOH HOH . 
E 5 HOH A 37 191 37 HOH HOH . 
E 5 HOH A 38 192 38 HOH HOH . 
E 5 HOH A 39 193 39 HOH HOH . 
E 5 HOH A 40 194 40 HOH HOH . 
E 5 HOH A 41 195 41 HOH HOH . 
E 5 HOH A 42 196 42 HOH HOH . 
E 5 HOH A 43 197 43 HOH HOH . 
E 5 HOH A 44 198 44 HOH HOH . 
E 5 HOH A 45 199 45 HOH HOH . 
E 5 HOH A 46 200 46 HOH HOH . 
E 5 HOH A 47 201 47 HOH HOH . 
E 5 HOH A 48 202 48 HOH HOH . 
E 5 HOH A 49 203 49 HOH HOH . 
E 5 HOH A 50 204 50 HOH HOH . 
E 5 HOH A 51 205 51 HOH HOH . 
E 5 HOH A 52 206 52 HOH HOH . 
E 5 HOH A 53 207 53 HOH HOH . 
E 5 HOH A 54 208 54 HOH HOH . 
E 5 HOH A 55 209 55 HOH HOH . 
E 5 HOH A 56 210 56 HOH HOH . 
E 5 HOH A 57 211 57 HOH HOH . 
E 5 HOH A 58 212 58 HOH HOH . 
E 5 HOH A 59 213 59 HOH HOH . 
E 5 HOH A 60 214 60 HOH HOH . 
E 5 HOH A 61 215 62 HOH HOH . 
E 5 HOH A 62 216 63 HOH HOH . 
E 5 HOH A 63 217 64 HOH HOH . 
E 5 HOH A 64 218 65 HOH HOH . 
E 5 HOH A 65 219 66 HOH HOH . 
E 5 HOH A 66 220 67 HOH HOH . 
E 5 HOH A 67 221 68 HOH HOH . 
E 5 HOH A 68 222 69 HOH HOH . 
E 5 HOH A 69 223 70 HOH HOH . 
E 5 HOH A 70 224 71 HOH HOH . 
E 5 HOH A 71 225 72 HOH HOH . 
E 5 HOH A 72 226 73 HOH HOH . 
E 5 HOH A 73 227 74 HOH HOH . 
E 5 HOH A 74 228 75 HOH HOH . 
E 5 HOH A 75 229 76 HOH HOH . 
E 5 HOH A 76 230 77 HOH HOH . 
E 5 HOH A 77 231 78 HOH HOH . 
E 5 HOH A 78 232 79 HOH HOH . 
E 5 HOH A 79 233 80 HOH HOH . 
E 5 HOH A 80 234 81 HOH HOH . 
E 5 HOH A 81 235 82 HOH HOH . 
E 5 HOH A 82 236 84 HOH HOH . 
E 5 HOH A 83 237 85 HOH HOH . 
E 5 HOH A 84 238 86 HOH HOH . 
E 5 HOH A 85 239 87 HOH HOH . 
E 5 HOH A 86 240 88 HOH HOH . 
E 5 HOH A 87 241 90 HOH HOH . 
E 5 HOH A 88 242 92 HOH HOH . 
E 5 HOH A 89 243 93 HOH HOH . 
E 5 HOH A 90 244 94 HOH HOH . 
E 5 HOH A 91 245 95 HOH HOH . 
E 5 HOH A 92 246 96 HOH HOH . 
E 5 HOH A 93 247 98 HOH HOH . 
E 5 HOH A 94 248 100 HOH HOH . 
E 5 HOH A 95 249 101 HOH HOH . 
E 5 HOH A 96 250 102 HOH HOH . 
E 5 HOH A 97 251 103 HOH HOH . 
E 5 HOH A 98 252 104 HOH HOH . 
E 5 HOH A 99 253 105 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N1 UMP . A . B 2 -4.898 57.329 30.913 0.3 17.8 ? N1 UMP 777 A 1 
HETATM 2 C C2 UMP . A . B 2 -3.725 56.829 30.367 0.3 18.56 ? C2 UMP 777 A 1 
HETATM 3 N N3 UMP . A . B 2 -2.885 57.681 29.674 0.3 16.97 ? N3 UMP 777 A 1 
HETATM 4 C C4 UMP . A . B 2 -3.19 59.022 29.536 0.3 17.45 ? C4 UMP 777 A 1 
HETATM 5 C C5 UMP . A . B 2 -4.373 59.534 30.084 0.3 16.87 ? C5 UMP 777 A 1 
HETATM 6 C C6 UMP . A . B 2 -5.222 58.667 30.775 0.3 17.7 ? C6 UMP 777 A 1 
HETATM 7 O O2 UMP . A . B 2 -3.419 55.619 30.481 0.3 18.9 ? O2 UMP 777 A 1 
HETATM 8 O O4 UMP . A . B 2 -2.421 59.754 28.916 0.3 17.66 ? O4 UMP 777 A 1 
HETATM 9 C C1' UMP . A . B 2 -5.789 56.412 31.661 0.3 17.99 ? C1' UMP 777 A 1 
HETATM 10 C C2' UMP . A . B 2 -5.77 56.792 33.147 0.3 17.81 ? C2' UMP 777 A 1 
HETATM 11 C C3' UMP . A . B 2 -7.09 57.513 33.354 0.3 17.91 ? C3' UMP 777 A 1 
HETATM 12 C C4' UMP . A . B 2 -7.983 56.871 32.301 0.3 16.71 ? C4' UMP 777 A 1 
HETATM 13 O O3' UMP . A . B 2 -7.615 57.337 34.658 0.3 18.05 ? O3' UMP 777 A 1 
HETATM 14 O O4' UMP . A . B 2 -7.135 56.508 31.23 0.3 18.82 ? O4' UMP 777 A 1 
HETATM 15 C C5' UMP . A . B 2 -9.06 57.811 31.78 0.3 18.02 ? C5' UMP 777 A 1 
HETATM 16 O O5' UMP . A . B 2 -8.46 58.906 31.136 0.3 15.71 ? O5' UMP 777 A 1 
HETATM 17 P P UMP . A . B 2 -8.914 60.397 31.546 0.3 14.74 ? P UMP 777 A 1 
HETATM 18 O OP1 UMP . A . B 2 -10.413 60.397 31.368 0.3 12.1 ? OP1 UMP 777 A 1 
HETATM 19 O OP2 UMP . A . B 2 -8.263 61.374 30.622 0.3 13.43 ? OP2 UMP 777 A 1 
HETATM 20 O OP3 UMP . A . B 2 -8.582 60.7 32.967 0.3 14.19 ? OP3 UMP 777 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#